Discovery of gene-regulation pathways using local causal search

Yoo C, Cooper GF.  Discovery of gene-regulation pathways using local causal search.  In: Proceedings of the Annual Symposium of the American Medical Informatics Association (2002) 914-918.  PMID:  12463958

This paper reports the methods and results of a computerbasedalgorithm that takes as input the expression levels of a set ofgenes as given by DNA microarray data, and then searches for causa lpathways that represent how the genes regulate each other. The algorithm uses local heuristic search anda Bayesian scoring metric.
We applied the algorithm to induce causal networksfrom a mixture of observational and experimental gene expression data on genes involved in galactose metabolism in the yeast Saccharomyces cerevisiae. The observational data consisted of gene-expression levels obtained from unmanipulated "wild-type" cells. The experimental data were produced by deleting ("knocking out') genes and measuring the expression levels of other genes. We used this data to evaluate several variations ofthe local search method. In each evaluation, causal relationships were predicted for all 36 pairwise combinations of nine key galactose-related genes. These predictions were then compared to the known causal relationships among these genes

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Yoo C, Cooper GF.
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